fix: soft delete empty repository records (batch 2)

mentioned in commit 7a9d6dad

mentioned in issue #596 (closed)

mentioned in merge request gitlab-org/build/CNG!898 (merged)

mentioned in merge request gitlab-com/gl-infra/k8s-workloads/gitlab-com!1534 (merged)

mentioned in merge request gitlab-com/gl-infra/k8s-workloads/gitlab-com!1535 (merged)

mentioned in merge request gitlab-org/charts/gitlab!2397 (merged)

mentioned in merge request omnibus-gitlab!5925 (merged)